Next-Generation Phage Display to Identify Peptide Ligands of Deubiquitinases

Spiliotopoulos, Anastasios; Maurer, Sigrun K.; Tsoumpeli, Maria T.; Bonfante, Juan A. F.; Owen, Jonathan P.; Gough, Kevin C.; Dreveny, Ingrid

Abstract

Phage display (PD) is a powerful method and has been extensively used to generate monoclonal antibodies and identify epitopes, mimotopes, and protein interactions. More recently, the combination of next-generation sequencing (NGS) with PD (NGPD) has revolutionized the capabilities of the method by creating large data sets of sequences from affinity selection-based approaches (biopanning) otherwise challenging to obtain. NGPD can monitor motif enrichment, allow tracking of the selection process over consecutive rounds, and highlight unspecific binders. To tackle the wealth of data obtained, bioinformatics tools have been developed that allow for identifying specific binding sequences (binders) that can then be validated. Here, we provide a detailed account of the use of NGPD experiments to identify ubiquitin-specific protease peptide ligands.

Citation

Spiliotopoulos, A., Maurer, S. K., Tsoumpeli, M. T., Bonfante, J. A. F., Owen, J. P., Gough, K. C., & Dreveny, I. (2023). Next-Generation Phage Display to Identify Peptide Ligands of Deubiquitinases. In J. Maupin-Furlow, & M. J. Edelmann (Eds.), Deubiquitinases: Methods and Protocols (189-218). Humana Press. https://doi.org/10.1007/978-1-0716-2803-4_12

• Online Publication Date: Nov 10, 2022
• Publication Date: 2023
• Deposit Date: Nov 10, 2022
• Publicly Available Date: Nov 11, 2024
• Publisher: Humana Press
• Pages: 189-218
• Series Title: Methods in Molecular Biology
• Series Number: 2591
• Book Title: Deubiquitinases: Methods and Protocols
• ISBN: 9781071628027
• DOI: https://doi.org/10.1007/978-1-0716-2803-4_12
• Public URL: https://nottingham-repository.worktribe.com/output/13460037
• Publisher URL: https://link.springer.com/protocol/10.1007/978-1-0716-2803-4_12